[BioC] Rgraphviz install problem

[Herve Pages]

Hi Shamit,

You seem to have the libdotneato.so.0 library under /usr/lib/graphviz
on your system but the dynamic loader doesn't "know" it...

If you are on a Linux system and if you have root access to it, you can
add this line
    /usr/lib/graphviz
to the /etc/ld.so.conf file and then run /sbin/ldconfig (you will need
root access for both: editing /etc/ld.so.conf and running /sbin/ldconfig).
This will add all the shared objects (the lib*.so.x.y.z files) found in
/usr/lib/graphviz to the list of registered shared objects.
Then try 'library(Rgraphviz)' again (you should not need to re-install
Rgraphviz).
Let me know if this doesn't work.

H.

Shamit Soneji wrote:

> Hi,
>
> I'm having trouble running Rgraphviz 1.8. The installation appears to go
> OK, but calling Rgraphviz in a session invokes the following error:
>
>> library(Rgraphviz)
>
> Loading required package: graph
> Loading required package: cluster
> Loading required package: Ruuid
> Error in dyn.load(x, as.logical(local), as.logical(now)) :
> unable to load shared library
> '/usr/local/lib/R/site-library/Rgraphviz/libs/Rgraphviz.so':
> libdotneato.so.0: cannot open shared object file: No such file or
> directory
> Error: .onLoad failed in 'loadNamespace' for 'Rgraphviz'
> Error: package/namespace load failed for 'Rgraphviz'
>
> ###########
>
> As far as I can tell I have all the dependencies installed above the
> minimum required version. The install looks like the following:
>
> ########
>
> # R CMD INSTALL Rgraphviz_1.8.0.tar.gz
> * Installing *source* package 'Rgraphviz' ...
> checking for graphviz... checking for
> dotneato-config... /usr/bin/dotneato-config
> /usr/bin/dotneato-config
> configure: creating ./config.status
> config.status: creating src/Makevars
> ** libs
> gcc -I/usr/lib/R/include -I/usr/include/graphviz -DGRAPHVIZGT_1_16
> -fPIC -g -O2 -c Rgraphviz.c -o Rgraphviz.o
> In file included from /usr/include/graphviz/render.h:53,
> from common.h:32,
> from Rgraphviz.c:1:
> /usr/include/graphviz/macros.h:41:1: warning: "NEW" redefined
> In file included from common.h:15,
> from Rgraphviz.c:1:
> /usr/lib/R/include/Rdefines.h:134:1: warning: this is the location of
> the previous definition
> gcc -I/usr/lib/R/include -I/usr/include/graphviz -DGRAPHVIZGT_1_16
> -fPIC -g -O2 -c RgraphvizInit.c -o RgraphvizInit.o
> In file included from /usr/include/graphviz/render.h:53,
> from common.h:32,
> from RgraphvizInit.c:1:
> /usr/include/graphviz/macros.h:41:1: warning: "NEW" redefined
> In file included from common.h:15,
> from RgraphvizInit.c:1:
> /usr/lib/R/include/Rdefines.h:134:1: warning: this is the location of
> the previous definition
> gcc -shared -o Rgraphviz.so Rgraphviz.o RgraphvizInit.o
> -L/usr/lib/graphviz -ldotneato -lm -L/usr/lib/R/lib -lR
> ** R
> ** inst
> ** save image
> Loading required package: graph
> Loading required package: cluster
> Loading required package: Ruuid
> Creating a new generic function for 'lines' in 'Rgraphviz'
> Creating a new generic function for 'plot' in 'Rgraphviz'
> .... the rest as per normal.
>
>
> Any ideas would be appreciated.
>
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